Novel nuclear and mitochondrial genetic markers have been developed and described in various species improving our ability to assess patterns of genetic variation within and among species and to reconstruct historical evolutionary events. The results have indicated the evolutionary history of leopards, jaguars, jaguarundis, tigers, giant pandas, guanacos, and Iberian lynx and limited levels of molecular genetic diversity among tigers and Iberian lynx. Analyses of nuclear genetic markers are refining our understanding of felid evolution and indicating the genetic basis of morphological traits such as melanism in the domestic cat. Concordant phylogenetic and phylogeographic studies of feline immunodeficiency virus transmission among free-ranging cat populations allows a glimpse of the process of emerging infections in species well suited for discovery of these events. Insight gained from these studies reveals evolved mechanisms for immune and natural defenses against fatal infections and neoplastic diseases.